Package Bio :: Package dbdefs :: Module medline
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Source Code for Module Bio.dbdefs.medline

 1  """Database definitions for retrieval of Medline information. 
 2  """ 
 3  from Bio.config.DBRegistry import DBGroup, EUtilsDB 
 4  from _support import * 
 5   
 6  from Martel import * 
 7   
 8  proxy_error_expr = has_expr(Alt(Str("500"), Str("502")) + Str(" Proxy Error")) 
 9  diagnostic_error_expr = has_str("WWW Error 500 Diagnostic") 
10  error_expr = Str("ERROR") 
11   
12  ncbi_failures=[ 
13      (proxy_error_expr, "proxy error"), 
14      (diagnostic_error_expr, "diagnostic error"), 
15      (error_expr, "ERROR"), 
16      (html_expr, "I got HTML and shouldn't have"), 
17      (Str("Please try again later"), "Please try again later"), 
18      (Str("The sequence has been intentionally withdrawn"), 
19       "Sequence withdrawn"), 
20      (blank_expr, "No data returned") 
21      ] 
22   
23  medline_eutils = EUtilsDB( 
24          name = "medline-eutils", 
25          doc = "Retrieve Medline data from NCBI using EUtils", 
26          delay = 5.0, 
27          db = "pubmed", 
28          rettype = "medline", 
29          failure_cases = ncbi_failures 
30          ) 
31   
32  medline = DBGroup( 
33          name = "medline", 
34          behavior = "serial") 
35  medline.add(medline_eutils) 
36